The Food and Drug Administration this week accused the drugmaker Pfizer of failing to properly investigate reports of malfunctioning EpiPens, including incidents when patients died or became severely ill after the device failed to work. Pfizer manufactures the EpiPen, which treats allergic reactions, for the drugmaker Mylan.

In a warning letter issued Tuesday, the agency said Meridian Medical Technologies, which is a unit of Pfizer, did not adequately look into problems with a crucial component of the EpiPen — the mechanism on the device that insures that it fires and delivers the proper dose of epinephrine, which stops an allergic reaction.

The F.D.A. said the company failed to conduct a proper investigation even though it received numerous complaints about problems with activating the device. “Our own data show that you received hundreds of complaints that your EpiPen products failed to operate during life-threatening emergencies, including some situations in which patients subsequently died,” the agency said in the letter.

A spokeswoman for Pfizer, Kim Bencker, said in a statement that the company was “very confident in the safety and efficacy of EpiPen products being produced at the site” and noted that it has shipped more than 30 million EpiPens since 2015. “It’s not unusual to receive product complaints, especially when the product is frequently administered by non-medically trained individuals.”

She added, “We currently have no information to indicate that there was any causal connection between these product complaints and any patient deaths.”

Theresa Eisenman, a spokeswoman for the F.D.A., did not provide details about the number of patient deaths reported, saying only that the agency had received “adverse event” reports that claimed the device failed to activate. She said “an adverse event report does not establish a causal relationship between an adverse event and device failure, and reports do not always contain enough detail to properly evaluate an event.”

In its letter, the F.D.A. noted that Pfizer and Mylan recalled 13 lots of the EpiPen earlier this year for products sold in the United States and overseas markets because of the problem, but said that the companies did so only after the F.D.A. inspected the manufacturing facility and “after multiple discussions with F.D.A.”

Nina Devlin, a spokeswoman for Mylan, said the company “has an unwavering commitment to quality and patient safety and we are confident in the safety and efficacy of EpiPen products being produced at the site.”

The warning letter is the latest bit of bad news for the EpiPen, which came under intense scrutiny a year ago following reports that Mylan had sharply raised the price of the product to more than $600 for a set of two injectors.

The outrage over the price increases led to Congressional inquiries and Mylan responded by releasing a generic version of the device that costs half as much.

In August, Mylan announced that it had finalized a $465 million settlement with the U.S. Department of Justice over claims that it overcharged the federal government for the product.